This tool processes raw sequence data to infer strain type and identify known drug resistance markers.

A stand alone version of this tool is now available and can now be run on linux or mac. Installation instructions can be found on GitHub and on the bioconda page.

This tool is for Research Use Only. Data and information provided through use of this tool are not intended for medical purpose or objective and should not be used for clinical diagnosis, patient management, or human clinical trials.

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Single nucleotide polymorphisms (SNPs) in coding regions are annotated using the reference amino acid, codon number and alternative amino acid (e.g. Ser315Thr in katG). SNPs in non-coding regions (i.e. RNA genes and intergenic regions) are annotated using the reference nucleotide, gene coordinate and alternative nucleotide (e.g. A1401G in rrs or C-37A in eis promoter). Indels are annotated using the reference VCF allele, gene coordinate and alternative VCF allele (e.g. T902TA insertion in katG).

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Drug1	Resistance	Supporting Mutations (frequency)
Isoniazid
Rifampicin
Ethambutol
Pyrazinamide
Streptomycin
Ethionamide
Fluoroquinolones
Amikacin
Capreomycin
Kanamycin

Lineage2	Family	Main Spoligotype	RDS
lineage4	Euro-American	LAM;T;S;X;H	None
lineage4.6	Euro-American	T;LAM	None
lineage4.6.2	Euro-American	T;LAM	RD726
lineage4.6.2.2	Euro-American (Cameroon)	LAM10-CAM	RD726

Gene	Chromosome Position	Mutation	Estimated fraction
gyrA	7362	p.Glu21Gln	1.000
gyrA	7585	p.Ser95Thr	1.000
gyrA	9304	p.Gly668Asp	1.000
rpsL	781395	c.-165T>C	1.000
rrs	1472172	r.327t>c	0.183
rrs	1472181	r.336g>a	0.168
rrs	1472214	r.369c>g	0.228
rrs	1472235	r.390g>c	0.198
rrs	1472240	r.395g>c	0.190
rrs	1472242	r.397c>t	0.186
rrs	1472251	r.406g>a	0.148
rrs	1472253	r.408g>t	0.152
rrs	1472259	r.414c>a	0.154
rrs	1472266	r.421c>a	0.144
rrs	1472338	r.493a>c	0.204
rrs	1472344	r.499c>t	0.224
rrs	1472349	r.504a>t	0.240
rrs	1472374	r.529t>a	0.228
rrs	1472379	r.534t>g	0.231
rrs	1472382	r.537g>t	0.237
rrs	1472391	r.546c>t	0.224
rrs	1472598	r.753a>t	0.186
rrs	1472616	r.771g>a	0.248
rrs	1472734	r.889c>t	0.202
rrs	1472741	r.896g>a	0.189
rrs	1472742	r.897c>t	0.212
rrs	1472781	r.936c>t	0.216
rrs	1472793	r.948a>t	0.216
rrs	1472803	r.958t>a	0.200
rrs	1472812	r.967a>c	0.197
rrs	1472887	r.1042g>c	0.236
rrs	1473038	r.1193a>c	0.252
rrs	1473044	r.1199c>g	0.241
rrs	1473173	r.1328c>t	0.185
rrs	1473177	r.1332g>a	0.238
rrs	1473202	r.1357c>t	0.250
rrl	1474199	r.542g>a	0.170
rrl	1474201	r.544t>c	0.170
rrl	1474202	r.545t>a	0.170
rrl	1474218	r.561t>a	0.224
rrl	1474228	r.571t>c	0.190
rrl	1474235	r.578g>c	0.174
rrl	1474249	r.592g>t	0.168
rrl	1474252	r.595t>a	0.162
rrl	1474264	r.607t>g	0.160
rrl	1474265	r.608g>a	0.160
rrl	1475526	r.1869c>t	0.174
rrl	1475538	r.1881t>c	0.135
rrl	1475539	r.1882a>t	0.141
rrl	1475540	r.1883c>t	0.141
rrl	1475545	r.1888t>g	0.137
rrl	1475571	r.1914a>t	0.168
rrl	1475707	r.2050t>c	0.148
rrl	1475713	r.2056c>g	0.150
rrl	1475716	r.2059a>t	0.144
rrl	1475803	r.2146t>c	0.224
rrl	1475804	r.2147g>c	0.224
rrl	1475816	r.2159c>g	0.248
rrl	1475817	r.2160a>g	0.250
rrl	1476252	r.2595t>g	0.140
rrl	1476260	r.2603a>g	0.137
rrl	1476266	r.2609g>a	0.140
rrl	1476336	r.2679c>g	0.214
rrl	1476356	r.2699c>g	0.208
rrl	1476357	r.2700t>a	0.222
rrl	1476358	r.2701t>c	0.176
rrl	1476382	r.2725a>g	0.195
rrl	1476384	r.2727g>t	0.204
rrl	1476404	r.2747g>a	0.209
rrl	1476408	r.2751g>a	0.261
rrl	1476442	r.2785t>a	0.210
rrl	1476443	r.2786g>t	0.225
rrl	1476455	r.2798c>a	0.191
rrl	1476456	r.2799a>t	0.189
rrl	1476466	r.2809c>t	0.214
rrl	1476470	r.2813c>t	0.222
rrl	1476474	r.2817c>t	0.184
rrl	1476481	r.2824t>c	0.188
tlyA	1917972	c.33A>G	1.000
thyX	3067474	p.Pro158Ala	1.000
alr	3841662	c.-242A>G	0.217
alr	3841663	c.-243G>A	0.214
embC	4242643	c.2781C>T	1.000
embB	4246584	p.Arg24Pro	0.600
ethA	4326739	c.735G>C	1.000
ethR	4328004	c.456G>A	1.000